A synthesis of dryland restoration techniques.

Purpose

To quantitatively examine the efficacy of vegetation restoration in drylands globally.

Questions

1. What is the global extent of research that directly examined restoration of drylands?
   
2. What were the common measures?
   
3. Is the restoration of vegetation a common and primary focus?
   
4. How frequently does the restoration measure outcomes beyond the focal species?
   
5. What were the primary restoration goals as reported by primary authors?
   
6. How much variation was there in the techniques tested and how long were experiments monitored and tested?
   
7. How relatively effective were the techniques?

Step 1. Search

Study-level viz to document patterns in exclusions primarily and the relatie frequenices, at the study level, of major categories of evidence.

#study data####
library(tidyverse)
studies <- read_csv("data/studies.csv")
studies

## # A tibble: 278 x 18
##       ID title technique data  region exclude rationale observations
##    <dbl> <chr> <chr>     <chr> <chr>  <chr>   <chr>     <chr>       
##  1   152 Shor~ seeding,~ expe~ Africa no      <NA>      <NA>        
##  2   180 Rest~ chemical~ App.~ Africa no      <NA>      <NA>        
##  3   229 Infl~ soil see~ fiel~ Africa no      <NA>      <NA>        
##  4   230 Acti~ planting  fiel~ Africa no      <NA>      <NA>        
##  5   255 The ~ grazing ~ fiel~ Africa no      <NA>      <NA>        
##  6   262 Reve~ seeding,~ eper~ Africa no      <NA>      <NA>        
##  7   263 The ~ phytogen~ fiel~ Africa no      <NA>      <NA>        
##  8   264 Eval~ seeding,~ fiel~ Africa no      <NA>      <NA>        
##  9   271 Patc~ natural ~ fiel~ Africa no      <NA>      <NA>        
## 10     4 Fact~ natural ~ App.~ Africa no      <NA>      <NA>        
## # ... with 268 more rows, and 10 more variables: disturbance <chr>,
## #   system <chr>, goal <chr>, intervention <chr>, paradigm <chr>,
## #   grazing <chr>, hypothesis <chr>, soil <chr>, benchmark <chr>,
## #   notes <chr>

#quick look at rationale needed
exclusions <- studies %>%
  filter(exclude == "yes")

#quick look at studies with paradigms
evidence <- studies %>%
  filter(exclude == "no")

#library(skimr)
#skim(evidence)

#study-level viz#####
#exclusions
ggplot(exclusions, aes(rationale, fill = region)) +
  geom_bar() +
  coord_flip() +
  labs(x = "rational for exclusion", y = "frequency") +
  scale_fill_brewer(palette = "Paired")

ggplot(evidence, aes(disturbance, fill = paradigm)) +
  geom_bar(na.rm = TRUE) +
  coord_flip() +
  scale_fill_brewer(palette = "Paired") +
  labs(y = "frequency")

ggplot(evidence, aes(region, fill = paradigm)) +
  geom_bar(na.rm = TRUE) +
  coord_flip() +
  scale_fill_brewer(palette = "Paired") +
  labs(y = "frequency")

ggplot(evidence, aes(data, fill = paradigm)) +
  geom_bar(na.rm = TRUE) +
  coord_flip() +
  scale_fill_brewer(palette = "Paired") +
  labs(y = "frequency")

ggplot(evidence, aes(system, fill = paradigm)) +
  geom_bar(na.rm = TRUE) +
  coord_flip() +
  scale_fill_brewer(palette = "Paired") +
  labs(y = "frequency")

ggplot(evidence, aes(goal, fill = paradigm)) +
  geom_bar(na.rm = TRUE) +
  coord_flip() +
  scale_fill_brewer(palette = "Paired") +
  labs(x = "outcome", y = "frequency")

#step 1 models####
#paradigm
derived.evidence <- evidence %>%
  group_by(technique, data, region, disturbance, goal, paradigm) %>% summarise(n = n())

#active-passive split
m <- glm(n~paradigm, family = poisson, derived.evidence)
anova(m, test="Chisq")

## Analysis of Deviance Table
## 
## Model: poisson, link: log
## 
## Response: n
## 
## Terms added sequentially (first to last)
## 
## 
##          Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL                       167     9.9147         
## paradigm  1 0.045115       166     9.8696   0.8318

#region
m1 <- glm(n~paradigm*region, family = poisson, derived.evidence)
#m1
#summary(m1)
anova(m1, test="Chisq")

## Analysis of Deviance Table
## 
## Model: poisson, link: log
## 
## Response: n
## 
## Terms added sequentially (first to last)
## 
## 
##                 Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL                              167     9.9147         
## paradigm         1 0.045115       166     9.8696   0.8318
## region           6 0.301367       160     9.5682   0.9995
## paradigm:region  6 0.213627       154     9.3546   0.9998

#outcome
m2 <- glm(n~paradigm*goal, family = poisson, derived.evidence)
#m1
#summary(m1)
anova(m2, test="Chisq")

## Analysis of Deviance Table
## 
## Model: poisson, link: log
## 
## Response: n
## 
## Terms added sequentially (first to last)
## 
## 
##               Df Deviance Resid. Df Resid. Dev Pr(>Chi)
## NULL                            167     9.9147         
## paradigm       1 0.045115       166     9.8696   0.8318
## goal           6 0.240941       160     9.6287   0.9997
## paradigm:goal  4 0.301480       156     9.3272   0.9897

#even split between active and passive evidence by all key categories

Step 2. Sort

A summary of sort process using PRISMA.

library(PRISMAstatement)
prisma(found = 1504,
       found_other = 5,
       no_dupes = 1039, 
       screened = 1039, 
       screen_exclusions = 861, 
       full_text = 178,
       full_text_exclusions = 101, 
       qualitative = 77, 
       quantitative = 66,
       width = 800, height = 800)

Step 3. Synthesize

Check data and calculate necessary measures.

#all data
#data <- read_csv("data/data.csv")
#data <- data %>%
  #mutate(lrr = log(mean.t/mean.c), rii = ((mean.t-mean.c)/(mean.t + mean.c)), var.es = ((sd.t^2/n.t*mean.t^2) + (sd.c^2/n.c*mean.c^2)))

#other effect size estimates
#library(compute.es)
#data <- data %>%
  #mutate(d=mes(mean.t, mean.c, sd.t, sd.c, n.t, n.c, level = 95, #cer = 0.2, dig = 2, , id = ID, data = data))
#check metafor

#all data
paperdata <- read_csv("data/paper_data.csv")
paperdata <- paperdata %>%
  mutate(lrr = log(mean.t/mean.c), rii = ((mean.t-mean.c)/(mean.t + mean.c)), var.es = ((sd.t^2/n.t*mean.t^2) + (sd.c^2/n.c*mean.c^2)))

Step 4. Summarize

Explore summary level data of all data. Explore aggregation levels that support the most reasonable data structure and minimize non-independence issues.

#evidence map####
require(maps)
world<-map_data("world")
map<-ggplot() + geom_polygon(data=world, fill="gray50", aes(x=long, y=lat, group=group))
map + geom_point(data=paperdata, aes(x=long, y=lat)) +
  labs(x = "longitude", y = "latitude") #render a literal map, i.e. evidence map, of where we study the niche in deserts globally

#add in levels and color code points on map####
map + geom_point(data=paperdata, aes(x=long, y=lat, color = paradigm)) + 
  scale_color_brewer(palette = "Paired") +
  labs(x = "longitude", y = "latitude", color = "")

#aggregation####
se <- function(x){
  sd(x)/sqrt(length(x))
}

data.simple <- paperdata %>%
  group_by(study.ID, paradigm, technique, measure.success) %>%
  summarise(n = n(), mean.lrr = mean(lrr), mean.rii = mean(rii), mean.var = mean(var.es))

main.data <- paperdata %>%
  group_by(study.ID, paradigm, intervention, outcome) %>%
  summarise(n = n(), mean.lrr = mean(lrr), mean.rii = mean(rii), mean.var = mean(var.es))


#EDA data####
simple.data <- paperdata %>% group_by(study.ID, paradigm, technique, measure.success) %>% summarise(mean.rii = mean(rii), error = se(rii))
simple.data <- na.omit(simple.data)

parad.data <- paperdata %>% group_by(study.ID, paradigm) %>% summarise(mean.rii = mean(rii), error = se(rii))
parad.data <- na.omit(parad.data)

tech.data <- paperdata %>% group_by(study.ID, technique) %>% summarise(mean.rii = mean(rii), error = se(rii))
tech.data <- na.omit(tech.data)

success.data <- paperdata %>% group_by(study.ID, measure.success) %>% summarise(mean.rii = mean(rii), error = se(rii))
success.data <- na.omit(success.data)


#active
active <- paperdata %>%
  filter(paradigm == "active")

#viz for aggregation####

disturbance.data <- paperdata %>% group_by(study.ID,disturbance, paradigm) %>% count()
disturbance.data2 <- disturbance.data %>% group_by(disturbance,paradigm) %>% count()
ggplot(na.omit(disturbance.data2), aes(disturbance,nn, fill=paradigm))+ geom_bar(stat = "identity") + coord_flip(ylim=0:44) + scale_fill_brewer(palette = "Blues")

ggplot(na.omit(data.simple), aes(technique, n, fill = paradigm)) + 
  geom_bar(stat = "identity") + 
  coord_flip() + 
  scale_fill_brewer(palette = "Paired")

ggplot(na.omit(data.simple), aes(measure.success, n, fill = paradigm)) + 
  geom_bar(stat = "identity") + 
  coord_flip() + 
  scale_fill_brewer(palette = "Paired")

#better
ggplot(main.data, aes(intervention, n, fill = paradigm)) + 
  geom_bar(stat = "identity") + 
  coord_flip() + 
  scale_fill_brewer(palette = "Paired") +
  labs(fill = "")

ggplot(main.data, aes(outcome, n, fill = paradigm)) + 
  geom_bar(stat = "identity") + 
  coord_flip() + 
  scale_fill_brewer(palette = "Paired") +
  labs(fill = "")

Step 5a. EDA

Exploratory data analyses to understand data and QA/QC using Rii.

Step 5b. Models

Meta and conventional statistical models to explore relative efficacy.

Step 5. Synthesis stats

#p-value meta
library(metap)
#all data for metas but cleaned for na's
mdata <- paperdata %>%
  filter(paradigm == "active") %>%
  filter(!is.na(lrr)) %>%
  filter(!is.na(var.es)) %>%
  filter(!is.na(n.t)) %>%
  filter(!is.na(p)) %>%
  filter(!is.na(intervention)) %>%
  filter(is.finite(lrr))

#aggregated data for metas var estimated with central tendency
#note - could also bootstrap mean variance here instead of arithematic mean
simple.mdata <- mdata %>%
  group_by(intervention) %>%
  summarise(lrr = mean(lrr), var.es = mean(var.es), n = mean(n.t))

simple.mdata.2 <- mdata %>%
  group_by(intervention, outcome) %>%
  summarise(lrr = mean(lrr), var.es = mean(var.es), n = mean(n.t))  

simple.mdata.var <- mdata %>%
  group_by(intervention) %>%
  summarise(lrr = mean(lrr), var.es = se(var.es), n = mean(n.t))

simple.mdata2.var <- mdata %>%
  group_by(intervention, outcome) %>%
  summarise(lrr = mean(lrr), var.es = se(var.es), n = mean(n.t))

#metas with p-values####
schweder(mdata$p)

sumz(p, data = mdata)

## sumz =  41.12464 p =  0

mdata %>%
  split(.$intervention) %>%
  purrr::map(~sumz(.$p)) 

## $`carbon amendment`
## sumz =  12.80103 p =  8.089988e-38 
## 
## $`mycorrhizal inoculation`
## sumz =  10.1732 p =  1.305983e-24 
## 
## $nutrients
## sumz =  9.350793 p =  4.349654e-21 
## 
## $planting
## sumz =  23.27758 p =  3.739763e-120 
## 
## $seeding
## sumz =  23.82834 p =  8.493511e-126 
## 
## $vegetation
## sumz =  6.86889 p =  3.235173e-12 
## 
## $`water addition`
## sumz =  13.53169 p =  5.082856e-42

sumlog(mdata$p)

## chisq =  4002.878  with df =  1438  p =  4.380539e-240

#metas with meta package on effect size measures####
library(meta)
#all data non-aggregated
m <- metagen(lrr, var.es, studlab = ID, byvar = intervention, data = mdata)
summary(m)

## Number of studies combined: k = 665
## 
##                                          95%-CI            z  p-value
## Fixed effect model   -0.0063 [-0.0063; -0.0063] -40590292.09        0
## Random effects model  0.2266 [ 0.1715;  0.2816]         8.07 < 0.0001
## 
## Quantifying heterogeneity:
## tau^2 = 0.1848; H = 21775022.93 [21775022.02; 21775023.84]; I^2 = 100.0% [100.0%; 100.0%]
## 
## Quantifying residual heterogeneity:
## H = 21874075.56 [21874074.65; 21874076.48]; I^2 = 100.0% [100.0%; 100.0%]
## 
## Test of heterogeneity:
##                      Q d.f. p-value
##  314836678046932224.00  664       0
## 
## Results for subgroups (fixed effect model):
##                                          k                     95%-CI
## intervention = planting                208 -0.0063 [-0.0063; -0.0063]
## intervention = carbon amendment         70 -1.2791 [-1.2845; -1.2738]
## intervention = vegetation               27  0.0008 [ 0.0008;  0.0008]
## intervention = nutrients                48 -0.0223 [-0.0717;  0.0272]
## intervention = seeding                 207 -0.0210 [-0.0210; -0.0210]
## intervention = mycorrhizal inoculation  30  0.7241 [ 0.7239;  0.7243]
## intervention = water addition           75  0.0037 [ 0.0025;  0.0049]
##                                                            Q   tau^2
## intervention = planting                314836590812084800.00  0.1848
## intervention = carbon amendment                      1618.90  0.0305
## intervention = vegetation                     61345019250.51  0.1134
## intervention = nutrients                               10.53       0
## intervention = seeding                        17441046877.02  0.0098
## intervention = mycorrhizal inoculation            2078953.52  0.0464
## intervention = water addition                         109.93 <0.0001
##                                           I^2
## intervention = planting                100.0%
## intervention = carbon amendment         95.7%
## intervention = vegetation              100.0%
## intervention = nutrients                 0.0%
## intervention = seeding                 100.0%
## intervention = mycorrhizal inoculation 100.0%
## intervention = water addition           32.7%
## 
## Test for subgroup differences (fixed effect model):
##                                    Q d.f. p-value
## Between groups         8446700545.63    6       0
## Within groups  314836669600231616.00  658       0
## 
## Results for subgroups (random effects model):
##                                          k                     95%-CI
## intervention = planting                208  0.4004 [ 0.3256;  0.4753]
## intervention = carbon amendment         70 -1.4672 [-1.6147; -1.3198]
## intervention = vegetation               27  0.3598 [ 0.0506;  0.6689]
## intervention = nutrients                48 -0.0223 [-0.0717;  0.0272]
## intervention = seeding                 207 -0.1585 [-0.1862; -0.1308]
## intervention = mycorrhizal inoculation  30  0.8426 [ 0.7533;  0.9319]
## intervention = water addition           75  0.0073 [-0.0012;  0.0158]
##                                                            Q   tau^2
## intervention = planting                314836590812084800.00  0.1848
## intervention = carbon amendment                      1618.90  0.0305
## intervention = vegetation                     61345019250.51  0.1134
## intervention = nutrients                               10.53       0
## intervention = seeding                        17441046877.02  0.0098
## intervention = mycorrhizal inoculation            2078953.52  0.0464
## intervention = water addition                         109.93 <0.0001
##                                           I^2
## intervention = planting                100.0%
## intervention = carbon amendment         95.7%
## intervention = vegetation              100.0%
## intervention = nutrients                 0.0%
## intervention = seeding                 100.0%
## intervention = mycorrhizal inoculation 100.0%
## intervention = water addition           32.7%
## 
## Test for subgroup differences (random effects model):
##                       Q d.f.  p-value
## Between groups   966.83    6 < 0.0001
## 
## Details on meta-analytical method:
## - Inverse variance method
## - DerSimonian-Laird estimator for tau^2

funnel(m)

#metabias(m)
#forest(m, sortvar = intervention)

m.study <- metagen(lrr, var.es, studlab = study.ID, byvar = intervention, data = mdata)
summary(m.study)

## Number of studies combined: k = 665
## 
##                                          95%-CI            z  p-value
## Fixed effect model   -0.0063 [-0.0063; -0.0063] -40590292.09        0
## Random effects model  0.2266 [ 0.1715;  0.2816]         8.07 < 0.0001
## 
## Quantifying heterogeneity:
## tau^2 = 0.1848; H = 21775022.93 [21775022.02; 21775023.84]; I^2 = 100.0% [100.0%; 100.0%]
## 
## Quantifying residual heterogeneity:
## H = 21874075.56 [21874074.65; 21874076.48]; I^2 = 100.0% [100.0%; 100.0%]
## 
## Test of heterogeneity:
##                      Q d.f. p-value
##  314836678046932224.00  664       0
## 
## Results for subgroups (fixed effect model):
##                                          k                     95%-CI
## intervention = planting                208 -0.0063 [-0.0063; -0.0063]
## intervention = carbon amendment         70 -1.2791 [-1.2845; -1.2738]
## intervention = vegetation               27  0.0008 [ 0.0008;  0.0008]
## intervention = nutrients                48 -0.0223 [-0.0717;  0.0272]
## intervention = seeding                 207 -0.0210 [-0.0210; -0.0210]
## intervention = mycorrhizal inoculation  30  0.7241 [ 0.7239;  0.7243]
## intervention = water addition           75  0.0037 [ 0.0025;  0.0049]
##                                                            Q   tau^2
## intervention = planting                314836590812084800.00  0.1848
## intervention = carbon amendment                      1618.90  0.0305
## intervention = vegetation                     61345019250.51  0.1134
## intervention = nutrients                               10.53       0
## intervention = seeding                        17441046877.02  0.0098
## intervention = mycorrhizal inoculation            2078953.52  0.0464
## intervention = water addition                         109.93 <0.0001
##                                           I^2
## intervention = planting                100.0%
## intervention = carbon amendment         95.7%
## intervention = vegetation              100.0%
## intervention = nutrients                 0.0%
## intervention = seeding                 100.0%
## intervention = mycorrhizal inoculation 100.0%
## intervention = water addition           32.7%
## 
## Test for subgroup differences (fixed effect model):
##                                    Q d.f. p-value
## Between groups         8446700545.63    6       0
## Within groups  314836669600231616.00  658       0
## 
## Results for subgroups (random effects model):
##                                          k                     95%-CI
## intervention = planting                208  0.4004 [ 0.3256;  0.4753]
## intervention = carbon amendment         70 -1.4672 [-1.6147; -1.3198]
## intervention = vegetation               27  0.3598 [ 0.0506;  0.6689]
## intervention = nutrients                48 -0.0223 [-0.0717;  0.0272]
## intervention = seeding                 207 -0.1585 [-0.1862; -0.1308]
## intervention = mycorrhizal inoculation  30  0.8426 [ 0.7533;  0.9319]
## intervention = water addition           75  0.0073 [-0.0012;  0.0158]
##                                                            Q   tau^2
## intervention = planting                314836590812084800.00  0.1848
## intervention = carbon amendment                      1618.90  0.0305
## intervention = vegetation                     61345019250.51  0.1134
## intervention = nutrients                               10.53       0
## intervention = seeding                        17441046877.02  0.0098
## intervention = mycorrhizal inoculation            2078953.52  0.0464
## intervention = water addition                         109.93 <0.0001
##                                           I^2
## intervention = planting                100.0%
## intervention = carbon amendment         95.7%
## intervention = vegetation              100.0%
## intervention = nutrients                 0.0%
## intervention = seeding                 100.0%
## intervention = mycorrhizal inoculation 100.0%
## intervention = water addition           32.7%
## 
## Test for subgroup differences (random effects model):
##                       Q d.f.  p-value
## Between groups   966.83    6 < 0.0001
## 
## Details on meta-analytical method:
## - Inverse variance method
## - DerSimonian-Laird estimator for tau^2

#funnel(m)
#metabias(m)
#forest(m, sortvar = intervention)

#aggregated data
m1 <- metagen(lrr, var.es, studlab = intervention, data = simple.mdata)
summary(m1)

## Number of studies combined: k = 7
## 
##                                       95%-CI    z p-value
## Fixed effect model   0.7569 [0.2559; 1.2579] 2.96  0.0031
## Random effects model 0.7569 [0.2559; 1.2579] 2.96  0.0031
## 
## Quantifying heterogeneity:
## tau^2 = 0; H = 1.00 [1.00; 1.00]; I^2 = 0.0% [0.0%; 0.0%]
## 
## Test of heterogeneity:
##     Q d.f. p-value
##  0.00    6  1.0000
## 
## Details on meta-analytical method:
## - Inverse variance method
## - DerSimonian-Laird estimator for tau^2

funnel(m1)

metabias(m1)
#forest(m, sortvar = intervention)

#different var estimate
m2 <- metagen(lrr, var.es, studlab = intervention, data = simple.mdata.var)
summary(m2)

## Number of studies combined: k = 7
## 
##                                       95%-CI    z  p-value
## Fixed effect model   0.7569 [0.5221; 0.9917] 6.32 < 0.0001
## Random effects model 0.7569 [0.5221; 0.9917] 6.32 < 0.0001
## 
## Quantifying heterogeneity:
## tau^2 = 0; H = 1.00 [1.00; 1.00]; I^2 = 0.0% [0.0%; 0.0%]
## 
## Test of heterogeneity:
##     Q d.f. p-value
##  0.00    6  1.0000
## 
## Details on meta-analytical method:
## - Inverse variance method
## - DerSimonian-Laird estimator for tau^2

funnel(m2)

metabias(m2)
#forest(m, sortvar = intervention)


m3 <- metagen(lrr, var.es, studlab = intervention, byvar = outcome, data = simple.mdata.2)
summary(m3)

## Number of studies combined: k = 14
## 
##                                       95%-CI    z p-value
## Fixed effect model   0.7569 [0.2559; 1.2579] 2.96  0.0031
## Random effects model 0.7569 [0.2559; 1.2579] 2.96  0.0031
## 
## Quantifying heterogeneity:
## tau^2 = 0; H = 1.00 [1.00; 1.00]; I^2 = 0.0% [0.0%; 0.0%]
## 
## Quantifying residual heterogeneity:
## H = 1.00 [1.00; 1.00]; I^2 = 0.0% [0.0%; 0.0%]
## 
## Test of heterogeneity:
##     Q d.f. p-value
##  0.00   13  1.0000
## 
## Results for subgroups (fixed effect model):
##                                    k        
## outcome = vegetation and habitat   5 -0.3732
## outcome = native species           4  0.7569
## outcome = soil quality             3 -0.2582
## outcome = invertebrate community   1  0.3101
## outcome = vegetation               1  0.9542
##                                                           95%-CI    Q
## outcome = vegetation and habitat [     -102.3869;      101.6405] 0.00
## outcome = native species         [        0.2559;        1.2579] 0.00
## outcome = soil quality           [    -2495.7200;     2495.2037] 0.00
## outcome = invertebrate community [-87021594.0357; 87021594.6560] 0.00
## outcome = vegetation             [ -1387092.6104;  1387094.5187] 0.00
##                                  tau^2  I^2
## outcome = vegetation and habitat     0 0.0%
## outcome = native species             0 0.0%
## outcome = soil quality               0 0.0%
## outcome = invertebrate community    --   --
## outcome = vegetation                --   --
## 
## Test for subgroup differences (fixed effect model):
##                   Q d.f. p-value
## Between groups 0.00    4  1.0000
## Within groups  0.00    9  1.0000
## 
## Results for subgroups (random effects model):
##                                    k        
## outcome = vegetation and habitat   5 -0.3732
## outcome = native species           4  0.7569
## outcome = soil quality             3 -0.2582
## outcome = invertebrate community   1  0.3101
## outcome = vegetation               1  0.9542
##                                                           95%-CI    Q
## outcome = vegetation and habitat [     -102.3869;      101.6405] 0.00
## outcome = native species         [        0.2559;        1.2579] 0.00
## outcome = soil quality           [    -2495.7200;     2495.2037] 0.00
## outcome = invertebrate community [-87021594.0357; 87021594.6560] 0.00
## outcome = vegetation             [ -1387092.6104;  1387094.5187] 0.00
##                                  tau^2  I^2
## outcome = vegetation and habitat     0 0.0%
## outcome = native species             0 0.0%
## outcome = soil quality               0 0.0%
## outcome = invertebrate community    --   --
## outcome = vegetation                --   --
## 
## Test for subgroup differences (random effects model):
##                     Q d.f. p-value
## Between groups   0.00    4  1.0000
## 
## Details on meta-analytical method:
## - Inverse variance method
## - DerSimonian-Laird estimator for tau^2

#funnel(m)
radial(m3)

#metabias(m2)
#forest(m, sortvar = intervention)

m4 <- metagen(lrr, var.es, studlab = intervention, byvar = outcome, data = simple.mdata2.var)
summary(m4)

## Number of studies combined: k = 14
## 
##                                       95%-CI    z  p-value
## Fixed effect model   0.7569 [0.5221; 0.9917] 6.32 < 0.0001
## Random effects model 0.7569 [0.5221; 0.9917] 6.32 < 0.0001
## 
## Quantifying heterogeneity:
## tau^2 = 0; H = 1.00 [1.00; 1.00]; I^2 = 0.0% [0.0%; 0.0%]
## 
## Quantifying residual heterogeneity:
## H = 1.00 [1.00; 1.00]; I^2 = 0.0% [0.0%; 0.0%]
## 
## Test of heterogeneity:
##     Q d.f. p-value
##  0.00   13  1.0000
## 
## Results for subgroups (fixed effect model):
##                                    k        
## outcome = vegetation and habitat   5 -0.3732
## outcome = native species           4  0.7569
## outcome = soil quality             3 -0.2567
## outcome = invertebrate community   1  0.3101
## outcome = vegetation               1  0.9542
##                                                           95%-CI    Q
## outcome = vegetation and habitat [      -56.3098;       55.5634] 0.00
## outcome = native species         [        0.5221;        0.9917] 0.00
## outcome = soil quality           [    -1355.4681;     1354.9548] 0.00
## outcome = invertebrate community [-73938869.3024; 73938869.9227] 0.00
## outcome = vegetation             [  -784939.0735;   784940.9818] 0.00
##                                  tau^2  I^2
## outcome = vegetation and habitat     0 0.0%
## outcome = native species             0 0.0%
## outcome = soil quality               0 0.0%
## outcome = invertebrate community    --   --
## outcome = vegetation                --   --
## 
## Test for subgroup differences (fixed effect model):
##                   Q d.f. p-value
## Between groups 0.00    4  1.0000
## Within groups  0.00    9  1.0000
## 
## Results for subgroups (random effects model):
##                                    k        
## outcome = vegetation and habitat   5 -0.3732
## outcome = native species           4  0.7569
## outcome = soil quality             3 -0.2567
## outcome = invertebrate community   1  0.3101
## outcome = vegetation               1  0.9542
##                                                           95%-CI    Q
## outcome = vegetation and habitat [      -56.3098;       55.5634] 0.00
## outcome = native species         [        0.5221;        0.9917] 0.00
## outcome = soil quality           [    -1355.4681;     1354.9548] 0.00
## outcome = invertebrate community [-73938869.3024; 73938869.9227] 0.00
## outcome = vegetation             [  -784939.0735;   784940.9818] 0.00
##                                  tau^2  I^2
## outcome = vegetation and habitat     0 0.0%
## outcome = native species             0 0.0%
## outcome = soil quality               0 0.0%
## outcome = invertebrate community    --   --
## outcome = vegetation                --   --
## 
## Test for subgroup differences (random effects model):
##                     Q d.f. p-value
## Between groups   0.00    4  1.0000
## 
## Details on meta-analytical method:
## - Inverse variance method
## - DerSimonian-Laird estimator for tau^2

#funnel(m)
radial(m4)

#metabias(m2)
#forest(m, sortvar = intervention)

forest(m1, sortvar = intervention, fontsize = 10, xlim = c(-2, 2))

forest(m2, sortvar = intervention, fontsize = 10, xlim = c(-2, 2))

forest(m3, sortvar = intervention, fontsize = 10, xlim = c(-2, 2))

forest(m4, sortvar = intervention, fontsize = 10, xlim = c(-2, 2))

#t-tests for lrr diff from 0
mdata %>%
  split(.$intervention) %>%
  purrr::map(~sumz(.$lrr)) 

## $`carbon amendment`
## sumz =  2.031395 p =  0.02110749 
## 
## $`mycorrhizal inoculation`
## sumz =  -0.4709042 p =  0.6811454 
## 
## $nutrients
## sumz =  6.392107 p =  8.180747e-11 
## 
## $planting
## sumz =  2.984449 p =  0.001420447 
## 
## $seeding
## sumz =  7.26085 p =  1.923328e-13 
## 
## $vegetation
## sumz =  4.163645 p =  1.566035e-05 
## 
## $`water addition`
## sumz =  1.52389 p =  0.06376814

#effect sizes plots
#need better ci estimates
ggplot(simple.mdata, aes(intervention, lrr)) +
  ylim(c(-2,2)) +
  geom_point(position = position_dodge(width = 0.5)) + 
  labs(x = "", y = "lrr") +
  coord_flip() +
  geom_errorbar(aes(ymin=lrr-var.es, ymax=lrr+var.es), width=.05, position = position_dodge(width = 0.5)) +
  geom_hline(yintercept = 0, colour="grey", linetype = "longdash")

ggplot(simple.mdata.2, aes(intervention, lrr, color = outcome)) +
  ylim(c(-2,2)) +
  geom_point(position = position_dodge(width = 0.5)) + 
  labs(x = "", y = "lrr", color = "") +
  coord_flip() +
  geom_errorbar(aes(ymin=lrr-var.es, ymax=lrr+var.es), width=.05, position = position_dodge(width = 0.5)) +
  geom_hline(yintercept = 0, colour="grey", linetype = "longdash")

ggplot(mdata, aes(lrr, color = intervention)) +
  geom_freqpoly(binwidth = 0.5, size = 2) + 
  xlim(c(-10, 10)) +
  labs(x = "lrr", y = "frequency", color = "") +
  geom_vline(xintercept = 0, colour="grey", linetype = "longdash") +
  scale_color_brewer()

ggplot(mdata, aes(lrr, fill = intervention)) +
  geom_dotplot(binwidth = 1) + 
  xlim(c(-10, 10)) +
  labs(x = "lrr", y = "frequency", fill = "") +
  geom_vline(xintercept = 0, colour="grey", linetype = "longdash") +
  scale_fill_brewer()